Well, no real idea here. My guess is that IRanges is bringing in one copy,
and the UCSC stuff another.

Michael

On Sun, Nov 13, 2011 at 10:50 AM, rcaloger <raffaele.calogero@gmail.com>wrote:

> Dear all,
> I am trying to install rtracklayer on my server running linux suse
> enterprise 10
> any suggestion how to solve the problem?
> cheers
> raffaele
>
> source("http://bioconductor.**org/biocLite.R<http://bioconductor.org/biocLite.R>
> ")
> biocLite("rtracklayer")
>
> gcc -std=gnu99 -I/home/calogero/bin/R-2.14.0/**lib64/R/include
> -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/mnt/raidDisk/calogero/**
> Documents/bin/R-2.14.0/lib64/**R/library/IRanges/include" -g -Dinline=""
> -fpic -g -O2 -c ucsc/udc.c -o ucsc/udc.o
> ucsc/udc.c: In function ‘udcInfoViaHttp’:
> ucsc/udc.c:405: warning: implicit declaration of function ‘strptime’
> ucsc/udc.c:405: warning: comparison between pointer and integer
> ......
> /usr/local/lib/gcc/x86_64-**unknown-linux-gnu/4.4.1/**
> include-fixed/bits/string2.h:**1235: multiple definition of `__strsep_1c'
> IRanges_stubs.o:/usr/local/**lib/gcc/x86_64-unknown-linux-**
> gnu/4.4.1/include-fixed/bits/**string2.h:1235: first defined here
> collect2: ld returned 1 exit status
> make: *** [rtracklayer.so] Error 1
> ERROR: compilation failed for package ‘rtracklayer’
> * removing ‘/mnt/raidDisk/calogero/**Documents/bin/R-2.14.0/lib64/**
> R/library/rtracklayer’
>
> The downloaded packages are in
> ‘/tmp/RtmpbcA6gw/downloaded_**packages’
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, ...) :
> installation of package ‘rtracklayer’ had non-zero exit status
>
>
> The IRanges
>
>
> > sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BiocInstaller_1.2.1
>
> loaded via a namespace (and not attached):
> [1] tools_2.14.0
> >
>
> --
>
> ------------------------------**----------
> Prof. Raffaele A. Calogero
> Bioinformatics and Genomics Unit
> MBC Centro di Biotecnologie Molecolari
> Via Nizza 52, Torino 10126
> tel.   ++39 0116706457
> Fax    ++39 0112366457
> Mobile ++39 3333827080
> email: raffaele.calogero@unito.it
>       raffaele[dot]calogero[at]**gmail[dot]com
> www:   http://www.bioinformatica.**unito.it<http://www.bioinformatica.unito.it>
>
> ______________________________**_________________
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